SWITCHING ON BRAIN-SPECIFIC ALTERNATIVE SPLICING WITH A MICRORNA

by
Eugene Makeyev and
Tom Maniatis

August 7th, 2007

Jiangwen Zhang, Monica Carrasco, Eugene Makeyev and Tom Maniatis

Cellular differentiation requires global changes in gene expression at both transcriptional and posttranscriptional levels. Posttranscriptional regulation provides a mechanism for rapid changes in the protein composition of cells, and is widely used during the development of the mammalian nervous system. Repression of protein synthesis by microRNAs (miRNAs) and the generation of new protein isoforms by alternative pre-mRNA splicing are well known examples of posttranscriptional control.

miRNAs are ~22 nucleotide long non-coding RNAs that act by repressing translation and/or by destabilizing mRNAs that contain miRNA-binding sites. A number of miRNAs are expressed in the nervous system but their functions are largely unknown. Alternative pre-mRNA splicing provides a mechanism for generating protein diversity and contributes to the establishment of neuronal identity and to the unique function of mature neurons. However, the regulatory network that underlies the transition from non-neuronal to nervous system-specific alternative splicing patterns is poorly understood.

In an exciting breakthrough the Maniatis lab has now identified a critical link between miRNA and alternative splicing in the nervous system. Specifically, they showed that an abundant neuron-specific miRNA called miR-124 directly targets mRNA encoding PTBP1, a global repressor of nervous system-specific alternative pre-mRNA splicing. Therefore, miR-124 regulates nervous system alternative splicing by controlling the levels of PTBP1. In addition, they found that PTBP1 controls the inclusion of a critical exon in the pre-mRNA of PTBP2, a PTBP1 homolog that is highly expressed in the nervous system. In the presence of PTBP1 the critical PTBP2 exon is not recognized by the splicing machinery, resulting in the generation of PTBP2 mRNA containing a premature stop codon. The presence of this stop codon results in the degradation by PTBP2 mRNA by a process known as Nonsense-Mediated Decay (NMD).

Accordingly, as miR-124 RNA accumulates during neuronal differentiation, PTBP1 levels decrease, and PTBP2 levels increase. PTBP1 and PTBP2 are closely related homologs that function in the regulation of alternative splicing, but their functional properties differ dramatically. As a result, the change in the ratio of PTBP1 to PTBP2 in the developing nervous system leads to a global transition of the pattern of alternative pre-mRNA splicing. Additional studies show that this transition is necessary but not sufficient for neuronal differentiation. Taken together, these studies identify a simple biphasic switch in alternative splicing consisting of miR-124, PTBP1 and PTBP2.

These findings provide important new insights into the mechanisms involved in neuronal differentiation, but many questions pertaining to the newly identified miRNA/alternative splicing interface remain to be answered. For example, how are the levels of miR-124 and other brain-specific miRNAs regulated in the developing nervous system? Does miR-124, which targets several hundred mRNAs, control the levels of other splicing regulators? Finally, what are the molecular mechanisms that allow PTBP1 and PTBP2 to control a variety of alternatively spliced exons? These questions, and others, are the focus of future studies.